If you're flying into Zagreb and flying out of Dubrovnik, but still want to visit Bosnia and Slovenia, I would go to Ljubljana from Zagreb, then head west from Ljubljana to Koper and Piran, then south thru Istria including Porec, Pula and Opatija, then Rijeka. I would continue down the beautiful coast and visiting the islands if you have time. Major cities on the way are Zadar, Sibenik, Split. Near Sibenik I would go inland to see the Krka National Park and the city of Skradin. From Split continue driving along the coast with a detour to Mostar and back into Dubrovnik. According to Google Maps, that whole trip, without stopping is about 18 hours. It should be doable in 12 days depending on how many stops you make.